Kernel Patching

Well, here is the worst problem we've been told about so far, and Suse, RedHat and Mandrake are all guilty of it to a lesser or greater degree.

First, they patch the kernel a lot (sometimes to add hooks to distribution specific configuration tools). This makes it so that it doesn't work with various drivers that come with new hardware, or which provide extended functionality.
Then they don't make their patch available outside their own download method so you can't patch a vanilla kernel into compatability.

The worst ones make two extra errors in addition to this. they make it so that their systems won't run a vanilla kernel, and they make their configuration tools dependant on those heavily patched kernels,
so if you do manage to get a vanilla kernel to work, your configuration tools stop working.

All very silly and unhelpfull, but more evidence suggests that it was mainly to do with the long delays between stable kernel versions giving them little choice but to back-port various features from the unstable version.

We thought that this was no longer such a problem with the more recent (2.6) development model, but a number of distributions still use what is basically a private fork of various software, including the kernel.
The most notable example is google, with android and a lot of other forked software.

The silliest example is the use of patched filesystem tools, where the filesystem creation tools use extended features, not by adding extra flags and having the tools use them, but by changing defaults which you can't turn off.
The worst example of this is those distributions where it is impossible to create compatable filesystems for external drives or Linux from Scratch.